pinecone: pinecone

Description Usage Arguments Examples

View source: R/pinecone.R

Description

Sub-lineage identification using a phylogentic tree with branch lengths indicating SNP distance.

Usage

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pinecone(tree, thresh, rthreshold, quiet = FALSE)

Arguments

tree

a phylo object

thresh

SNP threshold for sub-lineage identification.

rthreshold

The threhold number of ancestral nodes to the root each sub-lineage must have if they are to be declared as major sub-lineages

quiet

whether or not to print out extra information (default=FALSE)

Examples

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tree.file.name <- system.file("extdata", "pyjar.staph_ST2371_45_re_itol_7079_1_6_root.joint.tre", package = "rPinecone")
tree <- phytools::read.newick(tree.file.name)
pinecone(tree, 2, 3)

alexwailan/rpinecone documentation built on Sept. 24, 2020, 1:38 p.m.